Human Gene EPHB6 (ENST00000652003.1_5) from GENCODE V47lift37
  Description: EPH receptor B6, transcript variant 1 (from RefSeq NM_004445.6)
Gencode Transcript: ENST00000652003.1_5
Gencode Gene: ENSG00000106123.13_9
Transcript (Including UTRs)
   Position: hg19 chr7:142,552,838-142,568,846 Size: 16,009 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr7:142,560,986-142,568,657 Size: 7,672 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:142,552,838-142,568,846)mRNA (may differ from genome)Protein (1021 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F8WCM8_HUMAN
DESCRIPTION: SubName: Full=Ephrin type-B receptor 6;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: EPHB6
Diseases sorted by gene-association score: good syndrome (16)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -312.50741-0.422 Picture PostScript Text
3' UTR -50.70189-0.268 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001090 - Ephrin_rcpt_lig-bd_dom
IPR008979 - Galactose-bd-like

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00069 - Protein kinase domain
PF00536 - SAM domain (Sterile alpha motif)
PF01404 - Ephrin receptor ligand binding domain
PF07647 - SAM domain (Sterile alpha motif)
PF07699 - Tyrosine-protein kinase ephrin type A/B receptor-like
PF07714 - Protein tyrosine and serine/threonine kinase
PF14575 - Ephrin type-A receptor 2 transmembrane domain

SCOP Domains:
47769 - SAM/Pointed domain
49363 - Purple acid phosphatase, N-terminal domain
49265 - Fibronectin type III
49785 - Galactose-binding domain-like
56112 - Protein kinase-like (PK-like)
57184 - Growth factor receptor domain
57889 - Cysteine-rich domain

ModBase Predicted Comparative 3D Structure on F8WCM8
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0005003 ephrin receptor activity
GO:0005524 ATP binding

Biological Process:
GO:0001806 type IV hypersensitivity
GO:0002456 T cell mediated immunity
GO:0006468 protein phosphorylation
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0032092 positive regulation of protein binding
GO:0048013 ephrin receptor signaling pathway
GO:0050663 cytokine secretion
GO:0050798 activated T cell proliferation
GO:2000525 positive regulation of T cell costimulation

Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  KJ901411 - Synthetic construct Homo sapiens clone ccsbBroadEn_10805 EPHB6 gene, encodes complete protein.
D83492 - Homo sapiens mRNA for Eph-family protein, complete cds.
JD476324 - Sequence 457348 from Patent EP1572962.
JD523552 - Sequence 504576 from Patent EP1572962.
BC015495 - Homo sapiens EPH receptor B6, mRNA (cDNA clone IMAGE:3903473), with apparent retained intron.
BC051028 - Homo sapiens EPH receptor B6, mRNA (cDNA clone IMAGE:5167011), with apparent retained intron.
BC056159 - Homo sapiens EPH receptor B6, mRNA (cDNA clone IMAGE:6204336).
JD157937 - Sequence 138961 from Patent EP1572962.
JD540507 - Sequence 521531 from Patent EP1572962.
JD336947 - Sequence 317971 from Patent EP1572962.
JD307558 - Sequence 288582 from Patent EP1572962.
JD204130 - Sequence 185154 from Patent EP1572962.
JD057388 - Sequence 38412 from Patent EP1572962.
JD044509 - Sequence 25533 from Patent EP1572962.
JD145728 - Sequence 126752 from Patent EP1572962.
JD507785 - Sequence 488809 from Patent EP1572962.
BC047892 - Homo sapiens EPH receptor B6, mRNA (cDNA clone IMAGE:5186638), containing frame-shift errors.
JD492831 - Sequence 473855 from Patent EP1572962.
JD430020 - Sequence 411044 from Patent EP1572962.
JD218916 - Sequence 199940 from Patent EP1572962.
BC110606 - Homo sapiens EPH receptor B6, mRNA (cDNA clone MGC:129910 IMAGE:40028676), complete cds.
BC110607 - Homo sapiens EPH receptor B6, mRNA (cDNA clone MGC:129911 IMAGE:40028687), complete cds.
JD216154 - Sequence 197178 from Patent EP1572962.
JD302264 - Sequence 283288 from Patent EP1572962.
JD104409 - Sequence 85433 from Patent EP1572962.
JD372994 - Sequence 354018 from Patent EP1572962.
JD205568 - Sequence 186592 from Patent EP1572962.
JD436578 - Sequence 417602 from Patent EP1572962.
AB384684 - Synthetic construct DNA, clone: pF1KB0100, Homo sapiens EPHB6 gene for ephrin type-B receptor 6 precursor, complete cds, without stop codon, in Flexi system.
EU054308 - Homo sapiens EphB6 variant protein mRNA, complete cds, alternatively spliced.
AL832533 - Homo sapiens mRNA; cDNA DKFZp547H2116 (from clone DKFZp547H2116).
JD474609 - Sequence 455633 from Patent EP1572962.
JD186898 - Sequence 167922 from Patent EP1572962.
JD143769 - Sequence 124793 from Patent EP1572962.
JD478720 - Sequence 459744 from Patent EP1572962.
JD317558 - Sequence 298582 from Patent EP1572962.
JD135435 - Sequence 116459 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: EPHB6 , F8WCM8, F8WCM8_HUMAN, NM_004445, uc328tsn.1, uc328tsn.2
UCSC ID: ENST00000652003.1_5
RefSeq Accession: NM_004445.6
Protein: F8WCM8

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.